BASIL2022GV3HDT: Difference between revisions
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== Docking== | == Docking== | ||
We used POCASA to determine potential binding pockets within our protein and PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. However, this area was where dCMP binded with the highest affinity in PyRx. The amino acids interacting with the substrate within that area are.... | We used POCASA to determine potential binding pockets within our protein and PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. However, this area was where dCMP binded with the highest affinity in PyRx. The amino acids interacting with the substrate within that area are.... | ||
Also, there are other <scene name='90/904996/Hydrophobic_interactions/1'>amino acids</scene> (Gly21, Ser22, Gly23, Val27, Thr 142, Gln149, Arg150, Thr197, Leu200, Thr201) that help hold the substrate in place in the protein. | |||
However, these results may not be as accurate because during the docking process on PyRx, we were unsuccessful | However, these results may not be as accurate because during the docking process on PyRx, we were unsuccessful | ||
